| Previous changeset 57:fbff6786b2f6 (2022-06-07) Next changeset 59:491dc0cd6a0d (2025-03-26) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 716fba7fd96789c993382d1bebc593ad24f99f0a |
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modified:
tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/README.rst Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -136,6 +136,8 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.10.1+galaxy3 - Silenced ``deltablast`` warning about using ``-num_threads`` + with ``--subject`` (i.e. FASTA file from your history). 2.10.1+galaxy2 - Fixed ``dc-megablast`` option in ``ncbi_blastn_wrapper.xml`` wrapper from inserting ``-window_size`` twice when executing. 2.10.1+galaxy1 - Add tool `NCBI get species taxids` that wraps NCBI's |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -46,7 +46,7 @@ 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== -Most of these fields are given explicitly in the XML file, others some like +Most of these fields are given explicitly in the XML file, but some like the percentage identity and the number of gap openings must be calculated. Be aware that the sequence in the extended tabular output or XML direct from @@ -60,13 +60,11 @@ However, check this with "diff -b ..." since BLAST+ sometimes includes an extra space character (probably a bug). """ - from __future__ import print_function import os import re import sys - from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -152,7 +152,7 @@ <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database value=" /> + <param name="database" value="" /> <param name="evalue_cutoff" value="1e-8"/> <param name="blast_type" value="blastp" /> <param name="out_format" value="6"/> |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.10.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -92,7 +92,7 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ +ftp://ftp.jcvi.org/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see |
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| diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Jun 07 12:12:49 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 |
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| @@ -90,7 +90,7 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ +ftp://ftp.jcvi.org/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see |